python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_spleen_adult_male_cynomolgus_monkey-GSM5901074.end1.fastq.gz scATAC-Seq_of_spleen_adult_male_cynomolgus_monkey-GSM5901074.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_spleen_adult_male_cynomolgus_monkey-GSM5901074.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_liver_adult_male_cynomolgus_monkey_2-GSM5901072.end1.fastq.gz scATAC-Seq_of_liver_adult_male_cynomolgus_monkey_2-GSM5901072.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_liver_adult_male_cynomolgus_monkey_2-GSM5901072.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_kidney_adult_male_cynomolgus_monkey-GSM5901070.end1.fastq.gz scATAC-Seq_of_kidney_adult_male_cynomolgus_monkey-GSM5901070.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_kidney_adult_male_cynomolgus_monkey-GSM5901070.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_liver_adult_female_cynomolgus_monkey_1-GSM5901071.end1.fastq.gz scATAC-Seq_of_liver_adult_female_cynomolgus_monkey_1-GSM5901071.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_liver_adult_female_cynomolgus_monkey_1-GSM5901071.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_heart_adult_female_cynomolgus_monkey-GSM5901069.end1.fastq.gz scATAC-Seq_of_heart_adult_female_cynomolgus_monkey-GSM5901069.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_heart_adult_female_cynomolgus_monkey-GSM5901069.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_colon_adult_female_cynomolgus_monkey-GSM5901068.end1.fastq.gz scATAC-Seq_of_colon_adult_female_cynomolgus_monkey-GSM5901068.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_colon_adult_female_cynomolgus_monkey-GSM5901068.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_uterus_adult_female_cynomolgus_monkey-GSM5901075.end1.fastq.gz scATAC-Seq_of_uterus_adult_female_cynomolgus_monkey-GSM5901075.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_uterus_adult_female_cynomolgus_monkey-GSM5901075.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py scATAC-Seq_of_lung_adult_female_cynomolgus_monkey-GSM5901073.end1.fastq.gz scATAC-Seq_of_lung_adult_female_cynomolgus_monkey-GSM5901073.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_fascicularis-T2T-MFA8v1.0/bowtie-indexes/Macaca_fascicularis-T2T-MFA8v1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - scATAC-Seq_of_lung_adult_female_cynomolgus_monkey-GSM5901073.2x36mers.Macaca_fascicularis-T2T-MFA8v1.0.unique